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Article: High-resolution and real-time wastewater viral surveillance by Nanopore sequencing

TitleHigh-resolution and real-time wastewater viral surveillance by Nanopore sequencing
Authors
KeywordsMutation
Nanopore sequencing
SARS-CoV-2
Viral monitoring
Wastewater
Wastewater-based epidemiology
Issue Date1-Jun-2024
PublisherElsevier
Citation
Water Research, 2024, v. 256 How to Cite?
AbstractWastewater genomic sequencing stands as a pivotal complementary tool for viral surveillance in populations. While long-read Nanopore sequencing is a promising platform to provide real-time genomic data, concerns over the sequencing accuracy of the earlier Nanopore versions have somewhat restrained its widespread application in wastewater analysis. Here, we evaluate the latest improved version of Nanopore sequencing (R10.4.1), using SARS-CoV-2 as the model infectious virus, to demonstrate its effectiveness in wastewater viral monitoring. By comparing amplicon lengths of 400 bp and 1200 bp, we revealed that shorter PCR amplification is more suitable for wastewater samples due to viral genome fragmentation. Utilizing mock wastewater samples, we validated the reliability of Nanopore sequencing for variant identification by comparing it with Illumina sequencing results. The strength of Nanopore sequencing in generating real-time genomic data for providing early warning signals was also showcased, indicating that as little as 0.001 Gb of data can provide accurate results for variant prevalence. Our evaluation also identified optimal alteration frequency cutoffs (>50 %) for precise mutation profiling, achieving >99 % precision in detecting single nucleotide variants (SNVs) and insertions/deletions (indels). Monitoring two major wastewater treatment plants in Hong Kong from September 2022 to April 2023, covering over 4.5 million population, we observed a transition in dominant variants from BA.5 to XBB lineages, with XBB.1.5 being the most prevalent variants. Mutation detection also highlighted the potential of wastewater Nanopore sequencing in uncovering novel mutations and revealed links between signature mutations and specific variants. This study not only reveals the environmental implications of Nanopore sequencing in SARS-CoV-2 surveillance but also underscores its potential in broader applications including environmental health monitoring of other epidemic viruses, which could significantly enhance the field of wastewater-based epidemiology.
Persistent Identifierhttp://hdl.handle.net/10722/350458
ISSN
2023 Impact Factor: 11.4
2023 SCImago Journal Rankings: 3.596

 

DC FieldValueLanguage
dc.contributor.authorXu, Xiaoqing-
dc.contributor.authorDeng, Yu-
dc.contributor.authorDing, Jiahui-
dc.contributor.authorTang, Qinling-
dc.contributor.authorLin, Yunqi-
dc.contributor.authorZheng, Xiawan-
dc.contributor.authorZhang, Tong-
dc.date.accessioned2024-10-29T00:31:42Z-
dc.date.available2024-10-29T00:31:42Z-
dc.date.issued2024-06-01-
dc.identifier.citationWater Research, 2024, v. 256-
dc.identifier.issn0043-1354-
dc.identifier.urihttp://hdl.handle.net/10722/350458-
dc.description.abstractWastewater genomic sequencing stands as a pivotal complementary tool for viral surveillance in populations. While long-read Nanopore sequencing is a promising platform to provide real-time genomic data, concerns over the sequencing accuracy of the earlier Nanopore versions have somewhat restrained its widespread application in wastewater analysis. Here, we evaluate the latest improved version of Nanopore sequencing (R10.4.1), using SARS-CoV-2 as the model infectious virus, to demonstrate its effectiveness in wastewater viral monitoring. By comparing amplicon lengths of 400 bp and 1200 bp, we revealed that shorter PCR amplification is more suitable for wastewater samples due to viral genome fragmentation. Utilizing mock wastewater samples, we validated the reliability of Nanopore sequencing for variant identification by comparing it with Illumina sequencing results. The strength of Nanopore sequencing in generating real-time genomic data for providing early warning signals was also showcased, indicating that as little as 0.001 Gb of data can provide accurate results for variant prevalence. Our evaluation also identified optimal alteration frequency cutoffs (>50 %) for precise mutation profiling, achieving >99 % precision in detecting single nucleotide variants (SNVs) and insertions/deletions (indels). Monitoring two major wastewater treatment plants in Hong Kong from September 2022 to April 2023, covering over 4.5 million population, we observed a transition in dominant variants from BA.5 to XBB lineages, with XBB.1.5 being the most prevalent variants. Mutation detection also highlighted the potential of wastewater Nanopore sequencing in uncovering novel mutations and revealed links between signature mutations and specific variants. This study not only reveals the environmental implications of Nanopore sequencing in SARS-CoV-2 surveillance but also underscores its potential in broader applications including environmental health monitoring of other epidemic viruses, which could significantly enhance the field of wastewater-based epidemiology.-
dc.languageeng-
dc.publisherElsevier-
dc.relation.ispartofWater Research-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectMutation-
dc.subjectNanopore sequencing-
dc.subjectSARS-CoV-2-
dc.subjectViral monitoring-
dc.subjectWastewater-
dc.subjectWastewater-based epidemiology-
dc.titleHigh-resolution and real-time wastewater viral surveillance by Nanopore sequencing-
dc.typeArticle-
dc.identifier.doi10.1016/j.watres.2024.121623-
dc.identifier.pmid38657304-
dc.identifier.scopuseid_2-s2.0-85190892034-
dc.identifier.volume256-
dc.identifier.eissn1879-2448-
dc.identifier.issnl0043-1354-

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